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Crystal Structure of Myoferlin C2A with divalent cation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DMH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 310 orthorhombic shaped crystals
Crystal Properties Matthews coefficient Solvent content 2.17 43.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.35 α = 90 b = 83.11 β = 90 c = 94.28 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 315 2015-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.1271 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.929 62.345 99.8 0.109 0.112 0.135 0.06 9.5 4.8 28742
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 2.03 99.9 0.645 0.645 0.777 0.348 1.1 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2DMH 1.93 62.34 25836 2793 99.52 0.1857 0.1807 0.1922 0.232 0.2439 RANDOM 29.21
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.58 -0.53 1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.378 r_dihedral_angle_4_deg 17.921 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 7.204 r_angle_refined_deg 1.853 r_angle_other_deg 0.956 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.378 r_dihedral_angle_4_deg 17.921 r_dihedral_angle_3_deg 12.727 r_dihedral_angle_1_deg 7.204 r_angle_refined_deg 1.853 r_angle_other_deg 0.956 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3009 Nucleic Acid Atoms Solvent Atoms 473 Heterogen Atoms 6
Software Software Software Name Purpose DENZO data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing